chr=5
perl ../perl_flip_snp_basedreference_sample.pl -m ../ALL.chr$chr.20110521.b37p0.snps.markers.gz -s snps_chr$chr.bgl.gz  -n snps_chr$chr.bgl1.gz
mv snps_chr$chr.bgl1.gz snps_chr$chr.bgl.gz
chr=7
perl ../perl_flip_snp_basedreference_sample.pl -m ../ALL.chr$chr.20110521.b37p0.snps.markers.gz -s snps_chr$chr.bgl.gz  -n snps_chr$chr.bgl1.gz
mv snps_chr$chr.bgl1.gz snps_chr$chr.bgl.gz
chr=8
perl ../perl_flip_snp_basedreference_sample.pl -m ../ALL.chr$chr.20110521.b37p0.snps.markers.gz -s snps_chr$chr.bgl.gz  -n snps_chr$chr.bgl1.gz
mv snps_chr$chr.bgl1.gz snps_chr$chr.bgl.gz
chr=9
perl ../perl_flip_snp_basedreference_sample.pl -m ../ALL.chr$chr.20110521.b37p0.snps.markers.gz -s snps_chr$chr.bgl.gz  -n snps_chr$chr.bgl1.gz
mv snps_chr$chr.bgl1.gz snps_chr$chr.bgl.gz
chr=11
perl ../perl_flip_snp_basedreference_sample.pl -m ../ALL.chr$chr.20110521.b37p0.snps.markers.gz -s snps_chr$chr.bgl.gz  -n snps_chr$chr.bgl1.gz
mv snps_chr$chr.bgl1.gz snps_chr$chr.bgl.gz
chr=17
perl ../perl_flip_snp_basedreference_sample.pl -m ../ALL.chr$chr.20110521.b37p0.snps.markers.gz -s snps_chr$chr.bgl.gz  -n snps_chr$chr.bgl1.gz
mv snps_chr$chr.bgl1.gz snps_chr$chr.bgl.gz
chr=20
perl ../perl_flip_snp_basedreference_sample.pl -m ../ALL.chr$chr.20110521.b37p0.snps.markers.gz -s snps_chr$chr.bgl.gz  -n snps_chr$chr.bgl1.gz
mv snps_chr$chr.bgl1.gz snps_chr$chr.bgl.gz

